On Sept. 17, 2012, Chiheb Esseghaier and Raed Jaser drove to Jordan Station, a community in Niagara, Ont., wine country where the Maple Leaf train crosses a trestle bridge each day on its way from New York to Toronto.

Seven months later, the odd couple — one a Tunisian doctoral student, the other a school van driver and mover from Abu Dhabi — were arrested over what the RCMP has called an al-Qaeda-linked plot to derail a passenger train.

Most details of the alleged terrorism conspiracy remain under a court-ordered publication ban that prevents the press from reporting what the men, who are both in their 30s, are accused of doing and saying, and why they may have wanted to kill Canadians.

But some documents related to the case have now been partly unsealed by an Ontario judge at the request of the National Post and other media outlets, and they show the arrests followed a massive police undercover operation that spanned several countries.

Among the highlights that can now be revealed:

An RCMP constable and an FBI employee known as Tamer both infiltrated the alleged conspiracy early on and proved “very effective,” according to police.

In addition to Mr. Esseghaier and Mr. Jaser, two others were identified by police during the investigation in relation to terrorist activity but have not been arrested.

For Mr. Jaser, acquiring a rental house and land was “integral to his planning of terrorist acts,” the RCMP alleged.

Mr. Esseghaier had traveled to Iran prior to his arrest, the documents indicate. The RCMP has said the train plotters received “direction and guidance” from Al-Qaeda “elements” in Iran.

“The offences under investigation are terrorist acts which will cause loss of life and significant property damage,” the RCMP wrote to the court. “Esseghaier and Jaser have communicated about plans to commit a terrorist act in which the intent is to kill people.”

The suspects have not yet gone on trial so the police allegations have not been tested in court. Mr. Esseghaier, who has been trying to find a lawyer who will defend him according to Islamic law, did not object to the release of the documents.

Mr. Jaser’s lawyer declined to comment. “In view of the stage of the proceedings, it would not be appropriate for me to comment other than to reiterate that Mr. Jaser denies the allegations categorically,” John Norris said Friday.

The documents show that during the investigation, police went repeatedly before an Ontario judge to obtain warrants permitting them to do everything from marking evidence with invisible ink to staging break-ins to hide their covert searches.

Glenn Lowson photo for National Post

The warrants and the police information used to obtain them were sealed at the time to protect the investigation and undercover officers, but those passages that can now be disclosed depict an RCMP investigation that was sweeping, highly intrusive and ultra-secretive.

Although they went to great lengths to hide it, police had the suspects under a microscope long before the arrests last April. Not only were undercover officers and surveillance teams working the case, police also had judicial authorization to covertly search homes and cars, and monitor phones, computers and bank accounts.

“This is a complicated investigation,” Cpl. Patrick Flannery of the RCMP’s Toronto airport detachment wrote in a document filed in court. “This RCMP investigation is on-going, and involves other (unidentified) associates of Jaser and Esseghaier.”

Project Smooth appears to have gotten underway early in September, 2012. On Sept 4, police already had Mr. Jaser’s home in Toronto under surveillance. Officers were also digging into the backgrounds of their suspects, checking driver’s licence and immigration records.

Mr. Esseghaier was a landed immigrant who had come to Canada in 2008. A bio-nanotechnology student, he was working on his doctorate at the Institut National de la Recherche Scientifique, a branch of the Université de Quebec.

In the two years before his arrest, he had traveled to Zahedan, a city in eastern Iran that is frequented by al-Qaeda “facilitators” and serves as a gateway for fighters on their way to Afghanistan, the Reuters news agency has reported. The unsealed documents refer only generally to “Esseghaier’s travel to Iran.”

Glenn Lowson photo for National Post

Born in the United Arab Emirates to Palestinian parents, Mr. Jaser had lived in Germany before arriving in Canada with his family in 1993. Immigration authorities had tried to deport him in 2004 because of his criminal record.

But he was released because he was deemed stateless, meaning he had citizenship in no country and there was therefore nowhere else to send him. Like Mr. Esseghaier, he had recently become a landed immigrant.

Both men were known for their outspoken views on Muslim issues. At the lab where he worked, Mr. Esseghaier tore down posters he did not like and pestered administrators to install a prayer room, said a colleague, who described him as “brainwashed.”

Similarly, Mr. Jaser’s “radical talk” had disturbed Mohamed Ali, a part-time imam at the Masjid Al-Faisal mosque in Toronto. Another Muslim leader, Mohammed Robert Heft, said Mr. Jaser’s father had approached him over concerns his son “was becoming too rigid, he was becoming too self-righteous, too much of a know-it-all.”

Early in the investigation, Mr. Esseghaier traveled to Toronto and stayed with Mr. Jaser, the documents say. Despite car troubles, they made a Sept. 17 road trip to Jordan Station, Ont., where the New York-to-Toronto train crosses Jordan Harbour between St. Catharines and Grimsby daily at about 6:15 p.m.

Four days after the Jordan Station visit, the RCMP went to court to get a warrant to covertly enter the men’s homes and vehicles to look for “maps, pamphlets, brochures” and other documents on “the Canadian railway system.” They also wanted to try to identify any associates.

“The idea behind using a covert entry is to gather information without alerting Esseghaier, Jaser or anyone else to this ongoing police investigation,” the corporal wrote.

Investigators believed it was critical that no one found out about the investigation. If they did, they might destroy evidence or worse. Mr. Esseghaier and Mr. Jaser “are planning a terrorist act in which the intent is to kill people. If they learned that police plan to enter these locations, they may use it as an opportunity to attack those persons involved in the execution of this general warrant,” Cpl. Flannery wrote.

To prevent that from happening, police told the court they might need “to cause minor property damage” or take cash, electronics or even vehicles during their covert searches in order to “mask their actions” by making them look like break-ins. “The hope is that this ruse would prevent Esseghaier and Jaser or any other person from being alerted to the police investigation.”

If police found firearms or explosives during the searches, they were permitted to render them inoperable or replace them with “an inert substitute.” Officers were also allowed to “mark items with special ink, visible only under ultraviolet light, in order to identify them later.”

At the time, Mr. Jaser was working for Aplus School Services Ltd., driving kids to school in the Toronto suburb of Markham. Armed with their warrant, police conducted a covert entry of his Aplus vehicle on Oct. 2.

No evidence was found and the next day they secretly searched Mr. Jaser’s own car. This time they took photos of a book written in Arabic as well as screen shots of the locations that were stored on a GPS device.

In Montreal, meanwhile, police conducted a covert entry at Mr. Esseghaier’s apartment on Oct. 22. They copied his computer hard drive and took swabs “from multiple locations in the residence” for analysis.

But with the clock ticking on the warrant, investigators could find few opportunities to discretely carry out their searches. Mr. Esseghaier was preparing for an exam and spent more time studying at home than police had anticipated, and his roommate unexpectedly returned early from a trip.

Police also hoped to search Mr. Esseghaier’s lab but it was closed due to contamination, and investigators had “concerns over the ability to trust security staff.” Neither was it simple to get into Mr. Jaser’s house. His wife seldom went out and they lived in a multi-unit building, making it more challenging to conduct searches without being seen.

After the original warrant expired on Nov. 8, police went back to court for another one. It was granted on Nov. 12. Two days later they searched Mr. Jaser’s home and copied images from a video camera they found.

Police also obtained court orders compelling Rogers, Telus and Wind Mobile to hand over records on not only the phone calls and texts made by Mr. Esseghaier and Mr. Jaser, but also the locations of the cell towers closest to the phones when each call was made.

By April, police were ready to wrap up their operation. “A great deal of time has been spent planning the train derailment,” the RCMP wrote when it applied for warrants to conduct searches at the same time as the arrests.

The arrests were set for April 6. Mr. Esseghaier was to fly into Toronto that day from New York, where he had allegedly been meeting with an undercover officer and Ahmed Abassi, another Tunisian who had lived briefly in Quebec.

According to the FBI, while in the U.S., Mr. Esseghaier had discussed the train derailment and a scenario to kill up to 100,000 people by poisoning the air and water. But the RCMP had to put off their arrests.

“As a result of developments which had occurred within a parallel investigation being conducted by the Federal Bureau of Investigation, which also involved Esseghaier, the decision was to delay the arrests of Esseghaier and Jaser so as not to compromise the FBI investigation,” Cpl. Flannery explained to the Ontario court.

“Had Esseghaier and Jaser been arrested, the identity of an FBI undercover employee would have been compromised. This same FBI undercover employee has been working on the INSET investigation into Esseghaier and the FBI investigation involving Esseghaier and others in New York City. As a result, the search warrants were not executed.” INSET is the RCMP-led Integrated National Security Enforcement Team.

The RCMP waited more than two weeks before finally making their move on April 22, charging Mr. Esseghaier and Mr. Jaser with conspiracy to commit murder and terrorism offences. Mr. Abassi was arrested in New York that same day.